scVelo

中文導讀

scVelo 是 RNA velocity 的 workhorse baseline,提供 steady-state 跟 dynamical 兩種估計。 steady-state estimator 用 u–s phase portrait 的斜率定 γ(β≡1),所以本質上只拿得到 ratio; dynamical model 假設 α 是 piecewise on/off constant、β γ gene-specific constant,並給一個 gene-shared consensus latent time。對 physical time 來說它是 fully ungrounded 的參考點—— 後續方法(veloVI、RegVelo、dynamo)都是相對它在補不同的軸。

What it is

The standard-bearer RNA-velocity toolkit. Two estimators:

• Steady-state — fits γ as the slope of the unspliced–spliced phase portrait (β normalized to 1); identifies only the ratio β/γ.
• Dynamical — fits the full splicing-kinetics-ode per gene by EM (induction + repression
  • steady states) with a transcription switch (α piecewise on/off constant), gene-specific constant β, γ, and a gene-shared universal latent time (“internal clock”). Full source: scvelo-2020 (Bergen et al., Nat Biotechnol 2020, FabianTheis lab).
• Stochastic — moment-equation (second-order) variant; closed-form, scales to ~300k cells.

Scale degeneracy, admitted. scVelo itself states absolute kinetic rates are identifiable only with the overall developmental timescale as a prior — so its latent time defaults to a relative [0,1] ordering (scvelo-2020, Supp. Fig. 3). Fairer than “concept-swap” (xing-hu-regvelo-debate): the scale issue was named, but latent time became the de facto time axis downstream. It is a dynamics-grounded ordering (beats pseudotime — e.g. orders α- before β-cells), just not metric.

Physical-time scorecard

Axis	scVelo
Latent time	ordinal (consensus ordering)
Rate scale	ratios only (β≡1, steady-state) / relative constants (dynamical)
External anchor	none
Verdict	ungrounded (the baseline everything is measured against)

Role in the literature

The constant-rate, gene-independent baseline that newer methods relax: veloVI (deep-generative), RegVelo (GRN-coupled α), dynamo (labels → absolute rates). In benchmarks (regvelo) scVelo is consistently the reference for CBC, latent-time correlation, and TSI.

Related

scvelo-2020 · velocyto · RNA velocity · splicing-kinetics-ode · latent-time · physical-time-grounding · velocity-skepticism · veloVI · VeloVAE · RegVelo · dynamo · CellRank · FabianTheis